I'm sure there's an easy explanation to this.

Uncial 05 (Codex Bezae) and Uncial 06 (Codex Claromontanus) both have the letter 'D' assigned to them in the NA27 MS listing (pp. 691).

The texts are similar in that they are both Greek/Latin diglots, though Bezae is dated in the fifth century and Claromontanus in the sixth. (Metzger, Text of the New Testament 49-51) They do not have overlapping content; Bezae with Gospels/Acts (and a snippet of 3Jn) and Claromontanus with content from the Paulines.

Were these at one point considered to be the same MS? If not, why the same letter designator?

Quick checks of both Metzger and Aland didn't help with answering this question, apart from mentioning in passing that both MSS were in possession of Theodore Beza (though not stating if both texts were possessed by Beza at the same time).

Update: Thanks to James Tauber for the comment. It got me thinking — didn't the numbers come about with Caspar Rene Gregory's re-working of the whole system in the early 1900's, after his work on updating/completing Tischendorf's Edito Octava Maior? If so, the answer may be in Gregory's book (if it's in English ... ). Or is the uncial numbering an innovation of the Alands'?

Update II: And thanks as well to Stephen C. Carlson of Hypotyposeis for further clarification. I never realized that they re-used the uncial letters if there was no overlap between MS content.